Critical Reviews in Biochemistry and Molecular Biology最新文献_第6页

Structure and function of ClpXP, a AAA+ proteolytic machine powered by probabilistic ATP hydrolysis. 由概率ATP水解驱动的AAA+蛋白水解机ClpXP的结构和功能。

IF 6.5 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2022-04-01 DOI: 10.1080/10409238.2021.1979461

Robert T Sauer, Xue Fei, Tristan A Bell, Tania A Baker

引用次数: 11

Mitochondrial acute oxygen sensing and signaling. 线粒体急性氧传感和信号。

IF 6.5 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2022-04-01 Epub Date: 2021-12-01 DOI: 10.1080/10409238.2021.2004575

José López-Barneo, Patricia Ortega-Sáenz

{"title":"Mitochondrial acute oxygen sensing and signaling.","authors":"José López-Barneo, Patricia Ortega-Sáenz","doi":"10.1080/10409238.2021.2004575","DOIUrl":"https://doi.org/10.1080/10409238.2021.2004575","url":null,"abstract":"Oxygen (O2) is essential for life and therefore the supply of sufficient O2 to the tissues is a major physiological challenge. In mammals, a deficit of O2 (hypoxia) triggers rapid cardiorespiratory reflexes (e.g. hyperventilation and increased heart output) that within a few seconds increase the uptake of O2 by the lungs and its distribution throughout the body. The prototypical acute O2-sensing organ is the carotid body (CB), which contains sensory glomus cells expressing O2-regulated ion channels. In response to hypoxia, glomus cells depolarize and release transmitters which activate afferent fibers terminating at the brainstem respiratory and autonomic centers. In this review, we summarize the basic properties of CB chemoreceptor cells and the essential role played by their specialized mitochondria in acute O2 sensing and signaling. We focus on recent data supporting a \"mitochondria-to-membrane signaling\" model of CB chemosensory transduction. The possibility that the differential expression of specific subunit isoforms and enzymes could allow mitochondria to play a generalized adaptive O2-sensing and signaling role in a wide variety of cells is also discussed.","PeriodicalId":10794,"journal":{"name":"Critical Reviews in Biochemistry and Molecular Biology","volume":" ","pages":"205-225"},"PeriodicalIF":6.5,"publicationDate":"2022-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39771911","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 9

Diverse triterpene skeletons are derived from the expansion and divergent evolution of 2,3-oxidosqualene cyclases in plants. 2,3-氧化角鲨烯环化酶在植物体内的扩展和分化演化导致了不同的三萜骨架。

IF 6.5 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2022-04-01 Epub Date: 2021-10-02 DOI: 10.1080/10409238.2021.1979458

Jing Wang, Yanhong Guo, Xue Yin, Xiaoning Wang, Xiaoquan Qi, Zheyong Xue

{"title":"Diverse triterpene skeletons are derived from the expansion and divergent evolution of 2,3-oxidosqualene cyclases in plants.","authors":"Jing Wang, Yanhong Guo, Xue Yin, Xiaoning Wang, Xiaoquan Qi, Zheyong Xue","doi":"10.1080/10409238.2021.1979458","DOIUrl":"https://doi.org/10.1080/10409238.2021.1979458","url":null,"abstract":"Triterpenoids are one of the largest groups of secondary metabolites and exhibit diverse structures, which are derived from C30 skeletons that are biosynthesized via the isoprenoid pathway by cyclization of 2,3-oxidosqualene. Triterpenoids have a wide range of biological activities, and are used in functional foods, drugs, and as industrial materials. Due to the low content levels in their native plants and limited feasibility and efficiency of chemical synthesis, heterologous biosynthesis of triterpenoids is the most promising strategy. Herein, we classified 121 triterpene alcohols/ketones according to their conformation and ring numbers, among which 51 skeletons have been experimentally characterized as the products of oxidosqualene cyclases (OSCs). Interestingly, 24 skeletons that have not been reported from nature source were generated by OSCs in heterologous expression. Comprehensive evolutionary analysis of the identified 152 OSCs from 75 species in 25 plant orders show that several pentacyclic triterpene synthases repeatedly originated in multiple plant lineages. Comparative analysis of OSC catalytic reaction revealed that stabilization of intermediate cations, steric hindrance, and conformation of active center amino acid residues are primary factors affecting triterpene formation. Optimization of OSC could be achieved by changing of side-chain orientations of key residues. Recently, methods, such as rationally design of pathways, regulation of metabolic flow, compartmentalization engineering, etc., were introduced in improving chassis for the biosynthesis of triterpenoids. We expect that extensive study of natural variation of large number of OSCs and catalytical mechanism will provide basis for production of high level of triterpenoids by application of synthetic biology strategies.","PeriodicalId":10794,"journal":{"name":"Critical Reviews in Biochemistry and Molecular Biology","volume":" ","pages":"113-132"},"PeriodicalIF":6.5,"publicationDate":"2022-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39481164","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 19

Regulation of protein function and degradation by heme, heme responsive motifs, and CO. 血红素、血红素响应基序和一氧化碳对蛋白质功能和降解的调节。

IF 6.5 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2022-02-01 DOI: 10.1080/10409238.2021.1961674

Angela S Fleischhacker, Anindita Sarkar, Liu Liu, Stephen W Ragsdale

{"title":"Regulation of protein function and degradation by heme, heme responsive motifs, and CO.","authors":"Angela S Fleischhacker, Anindita Sarkar, Liu Liu, Stephen W Ragsdale","doi":"10.1080/10409238.2021.1961674","DOIUrl":"https://doi.org/10.1080/10409238.2021.1961674","url":null,"abstract":"Heme is an essential biomolecule and cofactor involved in a myriad of biological processes. In this review, we focus on how heme binding to heme regulatory motifs (HRMs), catalytic sites, and gas signaling molecules as well as how changes in the heme redox state regulate protein structure, function, and degradation. We also relate these heme-dependent changes to the affected metabolic processes. We center our discussion on two HRM-containing proteins: human heme oxygenase-2, a protein that binds and degrades heme (releasing Fe2+ and CO) in its catalytic core and binds Fe3+-heme at HRMs located within an unstructured region of the enzyme, and the transcriptional regulator Rev-erbβ, a protein that binds Fe3+-heme at an HRM and is involved in CO sensing. We will discuss these and other proteins as they relate to cellular heme composition, homeostasis, and trafficking. In addition, we will discuss the HRM-containing family of proteins and how the stability and activity of these proteins are regulated in a dependent manner through the HRMs. Then, after reviewing CO-mediated protein regulation of heme proteins, we turn our attention to the involvement of heme, HRMs, and CO in circadian rhythms. In sum, we stress the importance of understanding the various roles of heme and the distribution of the different heme pools as they relate to the heme redox state, CO, and heme binding affinities.","PeriodicalId":10794,"journal":{"name":"Critical Reviews in Biochemistry and Molecular Biology","volume":"57 1","pages":"16-47"},"PeriodicalIF":6.5,"publicationDate":"2022-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8966953/pdf/nihms-1788214.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9162339","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 7

Regulation of mRNA decay in E. coli. 大肠杆菌中 mRNA 的衰变调控。

IF 6.2 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2022-02-01 Epub Date: 2021-09-21 DOI: 10.1080/10409238.2021.1968784

Bijoy K Mohanty, Sidney R Kushner

{"title":"Regulation of mRNA decay in E. coli.","authors":"Bijoy K Mohanty, Sidney R Kushner","doi":"10.1080/10409238.2021.1968784","DOIUrl":"10.1080/10409238.2021.1968784","url":null,"abstract":"Detailed studies of the Gram-negative model bacterium, Escherichia coli, have demonstrated that post-transcriptional events exert important and possibly greater control over gene regulation than transcription initiation or effective translation. Thus, over the past 30 years, considerable effort has been invested in understanding the pathways of mRNA turnover in E. coli. Although it is assumed that most of the ribonucleases and accessory proteins involved in mRNA decay have been identified, our understanding of the regulation of mRNA decay is still incomplete. Furthermore, the vast majority of the studies on mRNA decay have been conducted on exponentially growing cells. Thus, the mechanism of mRNA decay as currently outlined may not accurately reflect what happens when cells find themselves under a variety of stress conditions, such as, nutrient starvation, changes in pH and temperature, as well as a host of others. While the cellular machinery for degradation is relatively constant over a wide range of conditions, intracellular levels of specific ribonucleases can vary depending on the growth conditions. Substrate competition will also modulate ribonucleolytic activity. Post-transcriptional modifications of transcripts by polyadenylating enzymes may favor a specific ribonuclease activity. Interactions with small regulatory RNAs and RNA binding proteins add additional complexities to mRNA functionality and stability. Since many of the ribonucleases are found at the inner membrane, the physical location of a transcript may help determine its half-life. Here we discuss the properties and role of the enzymes involved in mRNA decay as well as the multiple factors that may affect mRNA decay under various in vivo conditions.","PeriodicalId":10794,"journal":{"name":"Critical Reviews in Biochemistry and Molecular Biology","volume":"57 1","pages":"48-72"},"PeriodicalIF":6.2,"publicationDate":"2022-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9973670/pdf/nihms-1863991.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10798225","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Reprogramming of the epigenome in neurodevelopmental disorders. 神经发育障碍的表观基因组重编程。

IF 6.5 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2022-02-01 DOI: 10.1080/10409238.2021.1979457

Khadija D Wilson, Elizabeth G Porter, Benjamin A Garcia

{"title":"Reprogramming of the epigenome in neurodevelopmental disorders.","authors":"Khadija D Wilson, Elizabeth G Porter, Benjamin A Garcia","doi":"10.1080/10409238.2021.1979457","DOIUrl":"https://doi.org/10.1080/10409238.2021.1979457","url":null,"abstract":"The etiology of neurodevelopmental disorders (NDDs) remains a challenge for researchers. Human brain development is tightly regulated and sensitive to cellular alterations caused by endogenous or exogenous factors. Intriguingly, the surge of clinical sequencing studies has revealed that many of these disorders are monogenic and monoallelic. Notably, chromatin regulation has emerged as highly dysregulated in NDDs, with many syndromes demonstrating phenotypic overlap, such as intellectual disabilities, with one another. Here we discuss epigenetic writers, erasers, readers, remodelers, and even histones mutated in NDD patients, predicted to affect gene regulation. Moreover, this review focuses on disorders associated with mutations in enzymes involved in histone acetylation and methylation, and it highlights syndromes involving chromatin remodeling complexes. Finally, we explore recently discovered histone germline mutations and their pathogenic outcome on neurological function. Epigenetic regulators are mutated at every level of chromatin organization. Throughout this review, we discuss mechanistic investigations, as well as various animal and iPSC models of these disorders and their usefulness in determining pathomechanism and potential therapeutics. Understanding the mechanism of these mutations will illuminate common pathways between disorders. Ultimately, classifying these disorders based on their effects on the epigenome will not only aid in prognosis in patients but will aid in understanding the role of epigenetic machinery throughout neurodevelopment.","PeriodicalId":10794,"journal":{"name":"Critical Reviews in Biochemistry and Molecular Biology","volume":"57 1","pages":"73-112"},"PeriodicalIF":6.5,"publicationDate":"2022-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9462920/pdf/nihms-1832813.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9162784","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 8

The evolutionary history of the HUP domain. HUP结构域的进化历史。

IF 6.5 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2022-02-01 Epub Date: 2021-08-12 DOI: 10.1080/10409238.2021.1957764

Ita Gruic-Sovulj, Liam M Longo, Jagoda Jabłońska, Dan S Tawfik

{"title":"The evolutionary history of the HUP domain.","authors":"Ita Gruic-Sovulj, Liam M Longo, Jagoda Jabłońska, Dan S Tawfik","doi":"10.1080/10409238.2021.1957764","DOIUrl":"https://doi.org/10.1080/10409238.2021.1957764","url":null,"abstract":"Among the enzyme lineages that undoubtedly emerged prior to the last universal common ancestor is the so-called HUP, which includes Class I aminoacyl tRNA synthetases (AARSs) as well as enzymes mediating NAD, FAD, and CoA biosynthesis. Here, we provide a detailed analysis of HUP evolution, from emergence to structural and functional diversification. The HUP is a nucleotide binding domain that uniquely catalyzes adenylation via the release of pyrophosphate. In contrast to other ancient nucleotide binding domains with the αβα sandwich architecture, such as P-loop NTPases, the HUP's most conserved feature is not phosphate binding, but rather ribose binding by backbone interactions to the tips of β1 and/or β4. Indeed, the HUP exhibits unusual evolutionary plasticity and, while ribose binding is conserved, the location and mode of binding to the base and phosphate moieties of the nucleotide, and to the substrate(s) reacting with it, have diverged with time, foremost along the emergence of the AARSs. The HUP also beautifully demonstrates how a well-packed scaffold combined with evolvable surface elements promotes evolutionary innovation. Finally, we offer a scenario for the emergence of the HUP from a seed βαβ fragment, and suggest that despite an identical architecture, the HUP and the Rossmann represent independent emergences.","PeriodicalId":10794,"journal":{"name":"Critical Reviews in Biochemistry and Molecular Biology","volume":" ","pages":"1-15"},"PeriodicalIF":6.5,"publicationDate":"2022-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39305180","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 4

Ribosome-associated quality control and CAT tailing. 核糖体相关质量控制和CAT尾尾。

IF 6.5 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2021-12-01 Epub Date: 2021-07-07 DOI: 10.1080/10409238.2021.1938507

Conor J Howard, Adam Frost

{"title":"Ribosome-associated quality control and CAT tailing.","authors":"Conor J Howard, Adam Frost","doi":"10.1080/10409238.2021.1938507","DOIUrl":"https://doi.org/10.1080/10409238.2021.1938507","url":null,"abstract":"Translation is the set of mechanisms by which ribosomes decode genetic messages as they synthesize polypeptides of a defined amino acid sequence. While the ribosome has been honed by evolution for high-fidelity translation, errors are inevitable. Aberrant mRNAs, mRNA structure, defective ribosomes, interactions between nascent proteins and the ribosomal exit tunnel, and insufficient cellular resources, including low tRNA levels, can lead to functionally irreversible stalls. Life thus depends on quality control mechanisms that detect, disassemble and recycle stalled translation intermediates. Ribosome-associated Quality Control (RQC) recognizes aberrant ribosome states and targets their potentially toxic polypeptides for degradation. Here we review recent advances in our understanding of RQC in bacteria, fungi, and metazoans. We focus in particular on an unusual modification made to the nascent chain known as a \"CAT tail\", or Carboxy-terminal Alanine and Threonine tail, and the mechanisms by which ancient RQC proteins catalyze CAT-tail synthesis.","PeriodicalId":10794,"journal":{"name":"Critical Reviews in Biochemistry and Molecular Biology","volume":" ","pages":"603-620"},"PeriodicalIF":6.5,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/10409238.2021.1938507","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39161370","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 10

Isothermal amplifications - a comprehensive review on current methods. 等温扩增——对现有方法的综合评述。

IF 6.5 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2021-12-01 Epub Date: 2021-07-15 DOI: 10.1080/10409238.2021.1937927

Jörn Glökler, Theam Soon Lim, Jeunice Ida, Marcus Frohme

{"title":"Isothermal amplifications - a comprehensive review on current methods.","authors":"Jörn Glökler, Theam Soon Lim, Jeunice Ida, Marcus Frohme","doi":"10.1080/10409238.2021.1937927","DOIUrl":"https://doi.org/10.1080/10409238.2021.1937927","url":null,"abstract":"The introduction of nucleic acid amplification techniques has revolutionized the field of medical diagnostics in the last decade. The advent of PCR catalyzed the increasing application of DNA, not just for molecular cloning but also for molecular based diagnostics. Since the introduction of PCR, a deeper understanding of molecular mechanisms and enzymes involved in DNA/RNA replication has spurred the development of novel methods devoid of temperature cycling. Isothermal amplification methods have since been introduced utilizing different mechanisms, enzymes, and conditions. The ease with which isothermal amplification methods have allowed nucleic acid amplification to be carried out has had a profound impact on the way molecular diagnostics are being designed after the turn of the millennium. With all the advantages isothermal amplification brings, the issues or complications surrounding each method are heterogeneous making it difficult to identify the best approach for an end-user. This review pays special attention to the various isothermal amplification methods by classifying them based on the mechanistic characteristics which include reaction formats, amplification information, promoter, strand break, and refolding mechanisms. We would also compare the efficiencies and usefulness of each method while highlighting the potential applications and detection methods involved. This review will serve as an overall outlook on the journey and development of isothermal amplification methods as a whole.","PeriodicalId":10794,"journal":{"name":"Critical Reviews in Biochemistry and Molecular Biology","volume":" ","pages":"543-586"},"PeriodicalIF":6.5,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/10409238.2021.1937927","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39188051","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 47

Mechanisms of hexameric helicases. 六聚体螺旋酶的机制。

IF 6.5 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2021-12-01 Epub Date: 2021-08-17 DOI: 10.1080/10409238.2021.1954597

Amy J Fernandez, James M Berger

引用次数: 0